| abundanceContig | Demonstrate the relative abundance of clonotypes by group or sample. |
| addVariable | Adding variables after the combination of contigs. |
| alluvialClonotypes | Exploring interaction of clonotypes by seurat or SCE dynamics |
| checkContig | Assess the number of NAs in clonotypes |
| clonalDiversity | Examine the clonal diversity of samples |
| clonalHomeostasis | Examining the clonal homeostasis |
| clonalNetwork | Visualize clonal network along reduced dimensions |
| clonalOverlap | Examining the clonal overlap between groups or samples |
| clonalOverlay | Visualize distribution of clonal frequency overlaid on dimensional reduction plots |
| clonalProportion | Examining the clonal space occupied by specific clonotypes |
| clonesizeDistribution | Hierarchical clustering of clonotypes on clonotype size and Jensen-Shannon divergence |
| clonotypeBias | Examine clonotype bias |
| clusterTCR | Clustering T cell receptors |
| combineBCR | Combining the list of B Cell Receptor contigs |
| combineExpression | Adding clonotype information to a Seurat or SCE object |
| combineTCR | Combining the list of T Cell Receptor contigs |
| compareClonotypes | Demonstrate the difference in clonal proportion between clonotypes |
| contig_list | A data set of T cell contigs as a list outputed from the filter_contig_annotation files. |
| createHTOContigList | Generate a contig list from a multiplexed experiment |
| expression2List | Allows users to take the meta data in Seurat/SCE and place it into a list that will work with all the functions |
| getCirclize | Generate data frame to be used with circlize R package to visualize clonotypes as a chord diagram. |
| highlightClonotypes | Highlighting specific clonotypes in Seurat |
| lengthContig | Demonstrate the distribution of lengths filtered contigs. |
| loadContigs | Loading the contigs derived from single-cell sequencing |
| occupiedscRepertoire | Visualize the number of single cells with clonotype frequencies by cluster |
| quantContig | Quantify the unique clonotypes in the filtered contigs. |
| scatterClonotype | Scatter plot comparing the expansion of two samples |
| screp_example | A seurat object of 1000 single T cells derived from 3 clear cell renal carcinoma patients. |
| Startrac | The Startrac Class |
| Startrac-class | The Startrac Class |
| StartracDiversity | Diversity indices for single-cell RNA-seq |
| stripBarcode | Removing any additional prefixes to the barcodes of filtered contigs. |
| subsetContig | Subset the product of combineTCR() combineBCR() or expression2List() |
| vizGenes | Visualizing the distribution of gene usage |